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- PDB-1vs2: Interactions of quinoxaline antibiotic and DNA: the molecular str... -

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Basic information

Entry
Database: PDB / ID: 1vs2
TitleInteractions of quinoxaline antibiotic and DNA: the molecular structure of a TRIOSTIN A-D(GCGTACGC) complex
Components
  • 5'-D(*GP*CP*GP*TP*AP*CP*GP*C)-3'
  • TRIOSTIN A
KeywordsDNA/ANTIBIOTIC / BISINTERCALATOR / DESIPEPTIDE / QUINOXALINE / ANTIBIOTIC / ANTITUMOR / DNA-ANTIBIOTIC COMPLEX
Function / homologyTRIOSTIN A / 2-CARBOXYQUINOXALINE / : / DNA
Function and homology information
Biological speciesSTREPTOMYCINEAE (bacteria)
MethodX-RAY DIFFRACTION / Resolution: 2 Å
AuthorsWang, A.H.-J. / Ughetto, G. / Quigley, G.J. / Rich, A.
Citation
Journal: J.Biomol.Struct.Dyn. / Year: 1986
Title: Interactions of Quinoxaline Antibiotic and DNA: The Molecular Structure of a Triostin A-D(Gcgtacgc) Complex.
Authors: Wang, A.H. / Ughetto, G. / Quigley, G.J. / Rich, A.
#1: Journal: Science / Year: 1986
Title: Non-Watson-Crick G-C and A-T Base Pairs in a DNA-Antibiotic Complex
Authors: Quigley, G.J. / Ughetto, G. / Van Der Marel, G.A. / Van Boom, J.H. / Wang, A.H.-J. / Rich, A.
History
DepositionOct 21, 1986Deposition site: NDB / Processing site: NDB
Revision 1.0Jun 27, 2006Provider: repository / Type: Initial release
Revision 1.1Jun 14, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jul 27, 2011Group: Atomic model / Database references ...Atomic model / Database references / Derived calculations / Non-polymer description / Structure summary
Revision 1.4Feb 8, 2012Group: Derived calculations
Revision 1.5Feb 27, 2013Group: Other
Revision 1.6Dec 27, 2023Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_validate_polymer_linkage / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 5'-D(*GP*CP*GP*TP*AP*CP*GP*C)-3'
B: TRIOSTIN A
B: 2-CARBOXYQUINOXALINE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)3,5714
Polymers3,2232
Non-polymers3482
Water0
1
A: 5'-D(*GP*CP*GP*TP*AP*CP*GP*C)-3'
B: TRIOSTIN A
hetero molecules

A: 5'-D(*GP*CP*GP*TP*AP*CP*GP*C)-3'
B: TRIOSTIN A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)7,1428
Polymers6,4454
Non-polymers6974
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation9_555-x,-x+y,-z1
Buried area790 Å2
ΔGint-6.6 kcal/mol
Surface area3900 Å2
MethodPISA
Unit cell
Length a, b, c (Å)40.900, 40.900, 80.700
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number182
Space group name H-MP6322

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Components

#1: DNA chain 5'-D(*GP*CP*GP*TP*AP*CP*GP*C)-3'


Mass: 2427.605 Da / Num. of mol.: 1 / Source method: obtained synthetically
#2: Protein/peptide TRIOSTIN A


Type: Cyclic depsipeptide / Class: AnticancerAnticarcinogen / Mass: 794.982 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Details: TRIOSTIN IS A BICYCLIC OCTADEPSIPEPTIDE. BICYCLIZATION IS ACHIEVED BY LINKING THE N- AND THE C- TERMINI, AND A DISULPHIDE BOND BETWEEN RESIDUES 3 AND 7. THE TWO QUINOXALINE CHROMOPHORES ARE ...Details: TRIOSTIN IS A BICYCLIC OCTADEPSIPEPTIDE. BICYCLIZATION IS ACHIEVED BY LINKING THE N- AND THE C- TERMINI, AND A DISULPHIDE BOND BETWEEN RESIDUES 3 AND 7. THE TWO QUINOXALINE CHROMOPHORES ARE LINKED TO THE D-SERINE RESIDUES, RESIDUES 1 AND 5.
Source: (natural) STREPTOMYCINEAE (bacteria) / References: NOR: NOR01129, TRIOSTIN A
#3: Chemical ChemComp-QUI / 2-CARBOXYQUINOXALINE


Type: Cyclic depsipeptide / Class: AnticancerAnticarcinogen / Mass: 174.156 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C9H6N2O2
Details: TRIOSTIN IS A BICYCLIC OCTADEPSIPEPTIDE. BICYCLIZATION IS ACHIEVED BY LINKING THE N- AND THE C- TERMINI, AND A DISULPHIDE BOND BETWEEN RESIDUES 3 AND 7. THE TWO QUINOXALINE CHROMOPHORES ARE ...Details: TRIOSTIN IS A BICYCLIC OCTADEPSIPEPTIDE. BICYCLIZATION IS ACHIEVED BY LINKING THE N- AND THE C- TERMINI, AND A DISULPHIDE BOND BETWEEN RESIDUES 3 AND 7. THE TWO QUINOXALINE CHROMOPHORES ARE LINKED TO THE D-SERINE RESIDUES, RESIDUES 1 AND 5.
References: TRIOSTIN A
Compound detailsTRIOSTIN IS A BICYCLIC OCTADEPSIPEPTIDE, A MEMBER OF THE QUINOXALINE CLASS OF ANTIBIOTICS. HERE, ...TRIOSTIN IS A BICYCLIC OCTADEPSIPEPTIDE, A MEMBER OF THE QUINOXALINE CLASS OF ANTIBIOTICS. HERE, TRIOSTIN IS REPRESENTED BY GROUPING TOGETHER THE SEQUENCE (SEQRES) AND THE TWO LIGANDS (HET) QUI

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 3.84 Å3/Da / Density % sol: 67.94 %
Crystal growpH: 4.5 / Details: PH 4.50, VAPOR DIFFUSION
Components of the solutions
IDNameCrystal-IDSol-ID
1WATER11
2MPD11
3NA ACETATE11
4NACLSodium chloride11
5MGCL211
6SPERMINE11
7WATER12
8MPD12

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Data collection

DiffractionMean temperature: 285 K
DetectorType: NICOLET P3 / Detector: DIFFRACTOMETER
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionHighest resolution: 2 Å / Num. obs: 1130 / Observed criterion σ(I): 1.5

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Processing

SoftwareName: NUCLSQ / Classification: refinement
RefinementResolution: 2→10 Å /
RfactorNum. reflection
obs0.2 1130
Refine Biso Class: ALL ATOMS / Details: TR / Treatment: isotropic
Refinement stepCycle: LAST / Resolution: 2→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms52 161 24 0 237

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